[2024-01-25 19:08:35,841] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:35,842] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:35,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg75ad0132-0dc2-4606-811c-d3d704672616/dqc_reference
[2024-01-25 19:08:37,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:37,009] [INFO] Task started: Prodigal
[2024-01-25 19:08:37,010] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf6eb9f7-e876-4ea7-a493-bfa020db2a29/GCF_000741255.1_Bifmag_genomic.fna.gz | prodigal -d GCF_000741255.1_Bifmag_genomic.fna/cds.fna -a GCF_000741255.1_Bifmag_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:08:42,722] [INFO] Task succeeded: Prodigal
[2024-01-25 19:08:42,723] [INFO] Task started: HMMsearch
[2024-01-25 19:08:42,723] [INFO] Running command: hmmsearch --tblout GCF_000741255.1_Bifmag_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75ad0132-0dc2-4606-811c-d3d704672616/dqc_reference/reference_markers.hmm GCF_000741255.1_Bifmag_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:08:42,919] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:08:42,920] [INFO] Found 6/6 markers.
[2024-01-25 19:08:42,950] [INFO] Query marker FASTA was written to GCF_000741255.1_Bifmag_genomic.fna/markers.fasta
[2024-01-25 19:08:42,950] [INFO] Task started: Blastn
[2024-01-25 19:08:42,950] [INFO] Running command: blastn -query GCF_000741255.1_Bifmag_genomic.fna/markers.fasta -db /var/lib/cwl/stg75ad0132-0dc2-4606-811c-d3d704672616/dqc_reference/reference_markers.fasta -out GCF_000741255.1_Bifmag_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:43,790] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:43,793] [INFO] Selected 20 target genomes.
[2024-01-25 19:08:43,794] [INFO] Target genome list was writen to GCF_000741255.1_Bifmag_genomic.fna/target_genomes.txt
[2024-01-25 19:08:43,816] [INFO] Task started: fastANI
[2024-01-25 19:08:43,817] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf6eb9f7-e876-4ea7-a493-bfa020db2a29/GCF_000741255.1_Bifmag_genomic.fna.gz --refList GCF_000741255.1_Bifmag_genomic.fna/target_genomes.txt --output GCF_000741255.1_Bifmag_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:52,207] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:52,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75ad0132-0dc2-4606-811c-d3d704672616/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:52,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75ad0132-0dc2-4606-811c-d3d704672616/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:52,218] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:08:52,218] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:08:52,219] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Bifidobacterium magnum	strain=LMG 11591	GCA_000741255.1	1692	1692	type	True	100.0	600	600	95	conclusive
Bifidobacterium magnum	strain=DSM 20222	GCA_000420565.1	1692	1692	type	True	99.9729	589	600	95	conclusive
Bifidobacterium magnum	strain=DSM 20222	GCA_000771365.1	1692	1692	type	True	99.9631	575	600	95	conclusive
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_002706665.1	1690	1694	type	True	79.7601	250	600	95	below_threshold
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_000771145.1	1690	1694	type	True	79.7229	246	600	95	below_threshold
Bifidobacterium aerophilum	strain=TRE17	GCA_010667685.1	1798155	1798155	type	True	79.6464	227	600	95	below_threshold
Bifidobacterium gallicum	strain=DSM 20093	GCA_000173375.1	78342	78342	type	True	79.5858	221	600	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	79.461	228	600	95	below_threshold
Bifidobacterium castoris	strain=2020B	GCA_003952025.1	2306972	2306972	type	True	79.4426	241	600	95	below_threshold
Bifidobacterium gallicum	strain=DSM 20093	GCA_000771165.1	78342	78342	type	True	79.42	220	600	95	below_threshold
Bifidobacterium vansinderenii	strain=Tam10B	GCA_002234915.1	1984871	1984871	type	True	79.328	197	600	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	79.3214	225	600	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.2654	245	600	95	below_threshold
Bifidobacterium leontopitheci	strain=LMG 31471	GCA_009193355.1	2650774	2650774	type	True	79.2458	209	600	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	79.1531	235	600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:52,227] [INFO] DFAST Taxonomy check result was written to GCF_000741255.1_Bifmag_genomic.fna/tc_result.tsv
[2024-01-25 19:08:52,228] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:52,228] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:52,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75ad0132-0dc2-4606-811c-d3d704672616/dqc_reference/checkm_data
[2024-01-25 19:08:52,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:52,265] [INFO] Task started: CheckM
[2024-01-25 19:08:52,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000741255.1_Bifmag_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000741255.1_Bifmag_genomic.fna/checkm_input GCF_000741255.1_Bifmag_genomic.fna/checkm_result
[2024-01-25 19:09:12,896] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:12,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:12,916] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:12,916] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:12,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000741255.1_Bifmag_genomic.fna/markers.fasta)
[2024-01-25 19:09:12,916] [INFO] Task started: Blastn
[2024-01-25 19:09:12,916] [INFO] Running command: blastn -query GCF_000741255.1_Bifmag_genomic.fna/markers.fasta -db /var/lib/cwl/stg75ad0132-0dc2-4606-811c-d3d704672616/dqc_reference/reference_markers_gtdb.fasta -out GCF_000741255.1_Bifmag_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:14,056] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:14,059] [INFO] Selected 24 target genomes.
[2024-01-25 19:09:14,059] [INFO] Target genome list was writen to GCF_000741255.1_Bifmag_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:14,088] [INFO] Task started: fastANI
[2024-01-25 19:09:14,088] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf6eb9f7-e876-4ea7-a493-bfa020db2a29/GCF_000741255.1_Bifmag_genomic.fna.gz --refList GCF_000741255.1_Bifmag_genomic.fna/target_genomes_gtdb.txt --output GCF_000741255.1_Bifmag_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:23,854] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:23,867] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:23,867] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000741255.1	s__Bifidobacterium magnum	100.0	600	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	0.99	0.98	3	conclusive
GCF_010667615.1	s__Bifidobacterium choloepi	79.8747	293	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010425.1	s__Bifidobacterium adolescentis	79.798	220	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_004155535.1	s__Bifidobacterium pseudolongum_C	79.7974	251	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741295.1	s__Bifidobacterium globosum	79.7506	245	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.22	96.02	0.90	0.78	79	-
GCA_002451435.1	s__Bifidobacterium sp002451435	79.6773	189	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_010667685.1	s__Bifidobacterium aerophilum	79.635	227	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741205.1	s__Bifidobacterium gallicum	79.5966	217	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	1.00	0.99	4	-
GCF_001042635.1	s__Bifidobacterium scardovii	79.5076	233	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_002286915.1	s__Bifidobacterium italicum	79.5032	235	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952025.1	s__Bifidobacterium castoris	79.4426	241	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000771225.1	s__Bifidobacterium pseudolongum	79.3879	246	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.10	98.38	0.94	0.92	10	-
GCF_002234915.1	s__Galliscardovia vansinderenii	79.328	197	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932675.1	s__Bifidobacterium sp012932675	79.3103	207	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	79.2693	208	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000800455.1	s__Bifidobacterium kashiwanohense_A	79.2572	192	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.1942	N/A	N/A	N/A	N/A	1	-
GCF_003952005.1	s__Galliscardovia callimiconis	79.1866	187	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.12	98.12	0.92	0.92	2	-
GCF_000770925.1	s__Bifidobacterium ruminantium	79.1602	213	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_002860345.1	s__Bifidobacterium anseris	79.1096	238	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.21	99.21	0.95	0.95	2	-
GCF_001025135.1	s__Bifidobacterium bifidum	78.925	214	600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.04	98.27	0.95	0.91	128	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:23,869] [INFO] GTDB search result was written to GCF_000741255.1_Bifmag_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:23,869] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:23,872] [INFO] DFAST_QC result json was written to GCF_000741255.1_Bifmag_genomic.fna/dqc_result.json
[2024-01-25 19:09:23,873] [INFO] DFAST_QC completed!
[2024-01-25 19:09:23,873] [INFO] Total running time: 0h0m48s